Re: [babel] Evaluating all source blocks in a document?

[Rainer M Krug <r.m.krug@gmail.com>]

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Hi Eric

On Wed, Jun 30, 2010 at 4:55 PM, Erik Iverson <eriki@ccbr.umn.edu> wrote:

> Hello,
>
>
>     On Wed, Jun 30, 2010 at 01:35:04PM +0200, Rainer M Krug wrote:
>>     > Hi
>>     >
>>     > I use Org-babel for literate programming in R, but the tangling
>>    takes quite
>>     > long. Therefore my question: as it is possible to evaluate a
>>    single code
>>     > block, is it possible to evaluate ALL code blocks i a document?
>>    that would
>>     > make debugging much easier.
>>
>>    M-x org-babel-execute-buffer
>>
>>
> C-c C-v C-b should be a shortcut for that in org-mode now, according to my
> reference card.


Thanks - I was looking for that one.


>
>   Thanks - that  seems to be what I am looking for, but after trying it
>> out, I realized the following: for each block, e new R session is opened.
>> This does not work for literate programming, as different blocks belong to
>> each other, i.e. one block opens a function, the next one closes it. In
>> addition, I want to evaluate the results, i.e. created objects, in R -
>> therefore the session should stay open. So my guess: tangle and debug.
>>
>>    OTOH this may not make it easier to debug, the babel error window
>>    doesn't list line numbers or blocks where the error occurred.
>>
>
> Have you tried the :session argument?  It submits the code block to a
> running R session.  I use it for what you're doing with success.  You can
> set it per code block, or buffer-wide, try for example:
>
> #+PROPERTY: session *R*


No - I actually have not looked at that one before, but that is exactly what
I was looking for.

I'll come back if I have any further questions.

Thanks a lot,

Rainer


>
>
>
>>    Perhaps that should be a feature request to log what src block or
>>    org file
>>    line number the errors occurred in.
>>
>>
>> That would be nice.
>>
>>
>>     > Also: is it possible, to get some kind of automatic headings for
>>    the tangled
>>     > code blocks? That would make it easier to identify in which code
>>    block the
>>     > source code in the tangled file comes from.
>>
>
> Try
>
> (setq org-babel-tangle-w-comments t)
>
> and see if that does what you're thinking.  It will give headings for the
> source block, but I don't recall  what information they contain.
>



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Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
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